The most common bacterial infection identified in patients with AIDS is caused by Mycobacterium avium complex (MAC) bacilli. To rapidly and specifically detect MAC infections, polymerase chain reaction (PCR) protocols were developed. These protocols utilize PCR primers derived from unique sequences within the mycobacterial 16s RnA genes. Since the stool is a useful clinical specimen for detecting M. avium infections in AIDS patients, we have adapted our PCR protocols for use in evaluating stool samples. We have developed an immunomagnetic procedure which permits the rapid separation of M. avium bacilli from factors in the stool which inhibit the PCR. Thus far the PCR-immunomagnetic protocol has shown high specificity and sensitivity in assays using stool samples from thirty HIV patients. We anticipate that this protocol will be useful for the rapid identification of MAC infections in AIDS patients.